Source 1review2023Research
Toolkit/prime-editing
prime-editing
Also known as: DSB-free prime editors, PE, prime editing, prime editor, prime editors
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Prime editing is mentioned in the cited review as part of the broader set of genome-editing approaches considered in bacterial genome engineering. The supplied evidence does not describe its molecular architecture, target scope, or editing outcomes.
Usefulness & Problems
Why this is useful
The available evidence only supports that prime editing is considered within the landscape of bacterial genome-editing methods. No tool-specific utility, performance, or application examples are provided in the supplied text.
Problem solved
From the supplied evidence, prime editing is associated generally with genome editing in bacteria. The specific editing problem it solves, relative to other bacterial engineering methods, is not described.
Problem links
addresses limitations in CAR-T optimization
LiteratureThe abstract links prime editing to improving efficacy, managing toxicity, and improving accessibility in CAR-T therapy.
Source:
The abstract links prime editing to improving efficacy, managing toxicity, and improving accessibility in CAR-T therapy.
addresses precision limitations of CRISPR therapeutics
LiteratureIt is positioned as helping make CRISPR therapeutics safer and more precise in neurodegenerative disease settings.
Source:
It is positioned as helping make CRISPR therapeutics safer and more precise in neurodegenerative disease settings.
advancing precision genome editing options for posterior segment eye disease
LiteratureIt is intended to improve the precision of genome editing approaches for posterior segment eye diseases.
Source:
It is intended to improve the precision of genome editing approaches for posterior segment eye diseases.
avoids double-strand DNA cleavage or repair processes associated with conventional CRISPR-Cas editing
LiteratureIt expands the range of editable pathogenic variants beyond single-base conversion while avoiding double-strand DNA cleavage or repair. This is presented as beneficial in post-mitotic retinal cells.
Source:
It expands the range of editable pathogenic variants beyond single-base conversion while avoiding double-strand DNA cleavage or repair. This is presented as beneficial in post-mitotic retinal cells.
avoids need for exogenous donor templates
LiteratureIt addresses the need for precise correction of pathogenic point mutations or small indels, especially in ocular disorders. The review emphasizes that it can do so without double-stranded DNA breaks or donor DNA templates.
Source:
It addresses the need for precise correction of pathogenic point mutations or small indels, especially in ocular disorders. The review emphasizes that it can do so without double-stranded DNA breaks or donor DNA templates.
avoids requiring donor DNA templates
LiteratureIt addresses the need for precise genome editing while avoiding double-strand breaks and donor DNA templates, and it enables access to previously challenging mutations.
Source:
It addresses the need for precise genome editing while avoiding double-strand breaks and donor DNA templates, and it enables access to previously challenging mutations.
enables access to previously challenging mutations
LiteratureIt addresses the need for precise genome editing while avoiding double-strand breaks and donor DNA templates, and it enables access to previously challenging mutations.
Source:
It addresses the need for precise genome editing while avoiding double-strand breaks and donor DNA templates, and it enables access to previously challenging mutations.
enables precise genome editing without double-strand breaks
LiteratureIt addresses the need for precise genome editing while avoiding double-strand breaks and donor DNA templates, and it enables access to previously challenging mutations.
Source:
It addresses the need for precise genome editing while avoiding double-strand breaks and donor DNA templates, and it enables access to previously challenging mutations.
enables precise sequence changes without double-stranded DNA breaks
LiteratureIt addresses the need for precise correction of pathogenic point mutations or small indels, especially in ocular disorders. The review emphasizes that it can do so without double-stranded DNA breaks or donor DNA templates.
Source:
It addresses the need for precise correction of pathogenic point mutations or small indels, especially in ocular disorders. The review emphasizes that it can do so without double-stranded DNA breaks or donor DNA templates.
enabling precise and reversible genome-level modulation in psychiatric risk gene contexts
LiteratureIt addresses the need for precise and reversible modulation of psychiatric risk genes in design-biology workflows.
Source:
It addresses the need for precise and reversible modulation of psychiatric risk genes in design-biology workflows.
extends editing beyond single-nucleotide conversion to precise insertions and deletions
LiteratureIt expands the range of editable pathogenic variants beyond single-base conversion while avoiding double-strand DNA cleavage or repair. This is presented as beneficial in post-mitotic retinal cells.
Source:
It expands the range of editable pathogenic variants beyond single-base conversion while avoiding double-strand DNA cleavage or repair. This is presented as beneficial in post-mitotic retinal cells.
minimizing pleiotropic effects during genetic modification
LiteratureThe abstract specifically links it to minimizing pleiotropic effects.
Source:
The abstract specifically links it to minimizing pleiotropic effects.
modifying disease-causing genetic lesions in ocular disease contexts
LiteratureIt is framed as a strategy for modifying genetic ocular diseases. The review treats it as part of the therapeutic editing toolkit for eye disease.
Source:
It is framed as a strategy for modifying genetic ocular diseases. The review treats it as part of the therapeutic editing toolkit for eye disease.
provides a gene-editing approach for reactivating fetal hemoglobin-associated promoter states
LiteratureIt addresses the need for therapeutic strategies that increase HbF expression by rewriting b3-globin promoter sequence features toward HPFH-like states.
Source:
It addresses the need for therapeutic strategies that increase HbF expression by rewriting b3-globin promoter sequence features toward HPFH-like states.
reduces genomic damage in post-mitotic neurons
LiteratureIt is positioned as helping make CRISPR therapeutics safer and more precise in neurodegenerative disease settings.
Source:
It is positioned as helping make CRISPR therapeutics safer and more precise in neurodegenerative disease settings.
reducing or eliminating DSB-associated genotoxic stress from nuclease cutting
LiteratureIt is presented as reducing or eliminating DSB-associated genotoxic stress observed with nuclease cutting.
Source:
It is presented as reducing or eliminating DSB-associated genotoxic stress observed with nuclease cutting.
supports precise genetic modification in organoid systems
LiteratureIt contributes to precise modeling of human-specific pathologies and drug responses in organoid systems.
Source:
It contributes to precise modeling of human-specific pathologies and drug responses in organoid systems.
Published Workflows
Objective: Accelerate the development of climate-resilient Capsicum cultivars with optimized metabolic traits.
Why it works: The abstract argues that combining molecular insight from transcriptional, metabolic, and epigenetic analysis with precision phenotyping and genome editing should enable targeted reprogramming of regulatory loci that control adaptive responses and metabolic outputs.
transcription factor modulationosmotic adjustmentreactive oxygen species detoxificationhormonal crosstalksecondary metabolite biosynthesismulti-omics-guided gene discoveryprecision phenotypingCRISPR/Cas-mediated genome editingnext-generation genome editing
Stages
- 1.multi-omics-guided gene discovery(in_silico_filter)
The abstract positions multi-omics-guided gene discovery as the upstream step that identifies targets for subsequent genome editing.
Selection: Identification of key regulatory loci and stress-resilience frameworks from integrated transcriptional, metabolic, and epigenetic information.
- 2.precision phenotyping(functional_characterization)
The abstract includes precision phenotyping as a core component of the proposed framework linking molecular targets to cultivar-level performance.
Selection: Phenotypic assessment within the proposed framework for climate resilience and optimized metabolic traits.
- 3.next-generation genome editing(confirmatory_validation)
The abstract presents genome editing as the intervention step that operationalizes targets identified through transcription factor analysis and multi-omics-guided discovery.
Selection: Precise reprogramming of key regulatory loci to enhance adaptive responses.
Objective: Maximize prime editing efficiency and versatility across diverse cell types by systematically optimizing editor expression, pegRNA delivery, and related implementation variables.
Why it works: The abstract states that the combined strategy ensures robust, ubiquitous, and sustained expression of both prime editors and pegRNAs, which is presented as the basis for improved editing efficiency.
stable genomic integration of prime editorssustained expression of prime editors and pegRNAssystematic optimizationpiggyBac-mediated integrationsingle-clone selectionpromoter optimizationlentiviral pegRNA delivery
Stages
- 1.system optimization and build(library_build)
This stage exists to implement the optimization stack intended to maximize prime editing efficiency.
Selection: Combine stable editor integration, single-clone selection, enhanced promoter use, and lentiviral pegRNA delivery to improve prime editing performance.
- 2.performance assessment across loci and cell lines(functional_characterization)
This stage exists to determine whether the systematic optimizations improve editing efficiency broadly across test settings.
Selection: Assess editing efficiency across multiple loci and cell lines.
- 3.validation in challenging hPSC contexts(confirmatory_validation)
This stage exists to assess whether the optimized system remains effective in challenging cell types beyond the initial cell-line settings.
Selection: Test the optimized system in primed and naïve human pluripotent stem cells.
Steps
- 1.stably integrate prime editors using piggyBaceditor integration harness
Establish stable genomic integration of prime editors.
Stable editor integration is part of the optimization stack used to support robust and sustained expression before downstream validation.
- 2.select integrated single clones
Isolate single clones carrying the integrated editor system.
This follows editor integration because clone selection depends on having integrated cells to choose from.
- 3.use an enhanced promoter
Increase expression performance within the optimized prime editing system.
Promoter choice is part of the expression-optimization stack used to support robust and ubiquitous expression before performance testing.
- 4.deliver pegRNAs by lentiviruspegRNA delivery harness
Provide pegRNAs with robust, ubiquitous, and sustained expression.
PegRNA delivery is included as a key delivery optimization before evaluating editing outcomes.
- 5.measure editing efficiency across multiple loci and cell lines
Assess whether the optimization stack improves prime editing performance broadly.
Performance testing follows system construction so the combined optimizations can be evaluated.
- 6.validate the optimized system in primed and naïve hPSCs
Test whether the optimized system remains effective in challenging cell types.
This confirmatory validation is performed after broader cell-line testing to further assess efficacy in a more challenging context.
Objective: Automate molecular discovery and optimization in biofoundries by integrating AI into Design-Build-Test-Learn cycles.
Why it works: The abstract states that biofoundries integrate AI into DBTL cycles, automating molecular discovery and optimization.
AI integrationbiofoundry automationDesign-Build-Test-Learn workflow
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Architecture: A composed arrangement of multiple parts that instantiates one or more mechanisms.
Mechanisms
Degradationdouble-strand-break-free editingPhotocleavagereverse transcriptiontemplate-programmed genome editingTranslation ControlTarget processes
degradationeditinglocalizationmanufacturingrecombinationtranslationInput: Light
Implementation Constraints
cofactor dependency: requires exogenous cofactorencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: multi component delivery burdenimplementation constraint: payload burdenimplementation constraint: spectral hardware requirementoperating role: sensorswitch architecture: cleavageswitch architecture: multi componentswitch architecture: recruitment
No implementation details are provided for prime editing in the supplied evidence. There is no information on construct design, required proteins, guide formats, cofactors, or bacterial expression considerations.
The evidence base here is extremely limited and only documents mention of prime editing in a review. It provides no direct information on efficiency, edit types, host range, delivery, byproducts, or validation in bacterial systems.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Source 2primary paper2025MED
Source 3primary paper2026MED
Source 4primary paper2025MED
Source 5review2025MED
Source 6primary paper2025MED
Source 7review2025European Journal of Cell Biology
Source 8primary paper2026MED
Source 9review2021Microorganisms
Source 10primary paper2026MED
Source 11primary paper2025MED
Source 12review2026MED
Ranked Claims
Recent work in retinal cells and animal models has demonstrated growing feasibility of prime editing for inherited retinal disease treatment, modulation of pathological angiogenesis, and precise gene repair in post-mitotic photoreceptors and retinal pigment epithelial cells.
Prime editing is particularly relevant to ophthalmology because many blinding disorders arise from point mutations or small indels that are well suited to prime-editing correction.
CRISPR-associated transposases enable programmable targeted insertion strategies that can accommodate larger cassettes.
CRISPR-associated transposases now enable programmable, targeted insertion strategies that can accommodate larger cassettes
Prime editing enables precise genome correction by reverse-transcribing a template encoded in a pegRNA and can introduce substitutions and small indels in living cells without double-stranded DNA breaks or exogenous donor templates.
CAR-NK cells are a promising off-the-shelf alternative to CAR-T cells with a superior safety profile and inherent multi-antigen targeting capabilities.
Chimeric antigen receptor natural killer (CAR-NK) cells represent a promising "off-the-shelf" alternative to CAR-T cells, offering a superior safety profile and inherent multi-antigen targeting capabilities.
The review compares prime editing with CRISPR-Cas9 and Base editing as gene-editing strategies for HbF modulation.
This review also provides a comparative overview of prime editing and other gene-editing strategies for HbF modulation, such as CRISPR-Cas9 and Base editing.
Next-generation precision engineering tools are proposed to enhance three efficacy pillars in CAR-NK cells: persistence, trafficking, and tumor eradication.
These advanced technologies enable the precise enhancement of three fundamental pillars of efficacy: Persistence through endogenous cytokine armoring and metabolic engineering; Trafficking via chemokine receptor matching and stromal barrier degradation; and Tumor Eradication using logic-gated targeting, immunomodulatory payloads, and bispecific engagers.
Prime editing has emerged as an experimental approach capable of introducing multiple HPFH-like mutations within b3-globin promoters.
Regarding advances in b3-globin editing, "prime editing", although still in the experimental phase, has recently emerged as an innovative approach capable of introducing multiple HPFH-like mutations within b3-globin promoters...
Synthetic and epigenetic circuits provide dynamic context-dependent transgene control that avoids constitutive promoter-driven tonic signaling.
synthetic/epigenetic circuits provide dynamic, context-dependent transgene control that avoids constitutive promoter-driven tonic signaling
Promoter engineering and Prime Editing are expected to improve precision of soybean genetic modification and minimize pleiotropic effects.
The integration of new approaches, such as promoter engineering and Prime Editing, promises to further enhance the precision of genetic modifications, minimizing pleiotropic effects.
Editing SWEET10a and SWEET10b allows modulation of the soybean oil-protein balance.
the editing of sugar transporters SWEET10a and SWEET10b allows the modulation of the oil-protein balance
Inactivation of genes related to antinutritional factors has reduced expression of phytate and protease inhibitors in soybean.
Simultaneously, the inactivation of genes related to antinutritional factors has significantly reduced the expression of compounds such as phytate and protease inhibitors.
Silencing negative regulatory genes such as CIF1 and AIP2 can elevate soybean seed protein content.
Recent studies demonstrate that the silencing of negative regulatory genes, such as CIF1 and AIP2, can elevate the protein content of seeds
CAR-NK clinical potential is constrained by practical limitations of DSB-based CRISPR-Cas9, including chromosomal rearrangements, p53-mediated fitness loss, inefficient safe large multicistronic knock-ins, and rigid promoter-driven transgene expression that can cause tonic signaling.
their clinical potential is constrained by the "CRISPR ceiling", a set of practical limitations of DSB-based CRISPR-Cas9 such as DNA double-strand break (DSB)-associated chromosomal rearrangements and p53-mediated fitness loss, low efficiency for safe, large, multicistronic knock-ins, and rigid promoter-driven transgene expression that can cause tonic signaling.
DSB-free base and prime editors reduce or eliminate DSB-associated genotoxic stress compared with nuclease cutting.
next-generation, DSB-free base and prime editors reduce or eliminate the DSB-associated genotoxic stress observed with nuclease cutting
Engineering of Cas9 and reverse transcriptase domains, refinement of pegRNA architecture, recruitment of auxiliary proteins, and modulation of DNA repair pathways have enhanced prime-editing efficiency, product purity, and target scope across diverse cell types and tissues.
Prime editor generations from PE1 to PE7 and other next-generation variants are reported in the review to have increased in vitro editing efficiencies from 0.7 to 5.5% to more than 50%.
editing efficiency 0.7 to 5.5% to more than 50%
RNAi, CRISPR/Cas9, and AlphaFold2-guided gene editing are used to modify genes involved in carbon and nitrogen metabolism and storage proteins in soybean.
This work reviews the main progress achieved through transgenesis, induced mutagenesis, and precision gene editing, highlighting the role of tools such as RNAi, CRISPR/Cas9, and AlphaFold2-guided gene editing in modifying genes involved in carbon and nitrogen metabolism and storage proteins.
As delivery vectors and newer prime editor variants improve, prime editing is presented as a plausible next-generation platform for a wide range of ocular diseases.
Base editing, epigenetic reprogramming, targeted transposon systems, and synthetic biology circuits can be synergistically integrated to overcome critical clinical challenges in CAR-NK engineering.
We detail how base editing, epigenetic reprogramming, targeted transposon systems, and synthetic biology circuits can be synergistically integrated to overcome critical clinical challenges.
Structural modifications and improved delivery methods have expanded prime editing applicability across eukaryotic systems.
Through structural modifications and improved delivery methods, prime editing has expanded its applicability across eukaryotic systems.
CRISPR/Cas systems, base editing, and prime editing offer novel approaches to optimize CAR-T cells.
Base editing and prime editing provide alternatives for directly correcting pathogenic variants in inherited retinal diseases.
Recent breakthroughs in precision genome editing, particularly base editing (BE) and prime editing (PE), have provided alternatives capable of directly correcting pathogenic variants.
Prime editing enables precise genetic modifications without inducing double-strand breaks or requiring donor DNA templates.
Prime editing is an advanced genome editing technology that enables precise genetic modifications without inducing double-strand breaks or requiring donor DNA templates.
FDA approval of voretigene neparvovec validated the clinical viability of ocular gene therapy.
Base editing and prime editing circumvent double-strand DNA cleavage or repair processes typically induced by conventional CRISPR-Cas editing systems, offering advantages in post-mitotic retinal cells.
both circumventing the double-strand DNA cleavage or repair processes typically induced by conventional CRISPR-Cas editing systems, thereby offering advantages in post-mitotic retinal cells
Dual AAV vectors, lipid nanoparticles, and novel biomaterials have enhanced the efficiency and specificity of gene delivery to the retina.
CRISPR-based diagnostics such as SHERLOCK and DETECTR, together with AI-assisted sgRNA design and machine-learning off-target prediction, enhance the safety, stratification, and monitoring of CRISPR therapeutics.
Recent prime editing innovations enhance editing efficiency.
Here we examine the evolution of prime editing technologies, detailing advancements from the initial prime editing systems to recent innovations that enhance editing efficiency.
Future ocular gene therapy development is expected to include prime editing, miRNA-based regulation, and combinatorial approaches with stem cell transplantation or neuroprotective agents.
Emerging technologies including organoid fusion, xenografting, and optogenetics are expected to enhance understanding of cellular interactions and microenvironmental dynamics.
Leveraging gene editing has the potential to transform CAR-T therapy into a more potent, safer, and broadly applicable modality for cancer and beyond.
Clinical translation of base editing and prime editing for inherited retinal diseases is limited by low photoreceptor editing efficiency, interspecies variability, off-target risk, and large-scale vector manufacturing barriers.
critical challenges remain before clinical application can be realized, including limited editing efficiency in photoreceptors, interspecies variability in therapeutic response, potential risks of off-target effects, and barriers in large-scale vector manufacturing
Base editing enables targeted single-nucleotide conversions.
BE enables targeted single-nucleotide conversions
Prime editing allows precise insertions and deletions.
PE further allows for precise insertions and deletions
Base editing, prime editing, CRISPRi/a, and RNA-targeting Cas systems improve precision and reduce genomic damage, which is particularly advantageous in post-mitotic neurons.
Preclinical investigations in murine and non-human primate models have demonstrated feasibility, molecular accuracy, and preliminary safety profiles of base editing and prime editing platforms for targeting IRD-associated mutations.
Preclinical investigations across murine and non-human primate models have demonstrated the feasibility, molecular accuracy, and preliminary safety profiles of these platforms in targeting IRD-associated mutations.
Gene augmentation, gene editing, RNA-based therapies, and optogenetics have shown significant progress in preclinical studies and clinical trials across posterior segment eye disease subtypes.
Integration of genetic tools such as CRISPR-Cas9, prime editing, and lineage tracing has facilitated precise modeling of human-specific pathologies and drug responses in organoids.
Prime editing supports point mutations, insertions, and deletions.
Prime editing has rapidly become a versatile tool, supporting a wide range of genetic modifications, including point mutations, insertions and deletions.
Prime editing opens new avenues for therapeutic development and precision genetic research by enabling access to previously challenging mutations.
By enabling access to previously challenging mutations, prime editing opens new avenues for therapeutic development and precision genetic research.
The review covers characteristics of different AAV delivery routes in ocular clinical applications.
The review discusses progress of AAV in ocular optogenetic therapy.
The review outlines recent progress in AAV-mediated gene editing and silencing strategies for genetic ocular diseases, especially base editing and prime editing.
AAV is presented as one of the most promising viral gene delivery tools for ocular gene therapy because it can infect various tissue types and is considered relatively safe.
An increasing number of clinical trials of AAV-mediated gene therapy are underway for ocular diseases.
The eye is described as a favorable organ for AAV gene therapy because its limited volume is suitable for small doses that can achieve stable transduction.
The review identifies difficulties in the clinical transformation of AAV-mediated ocular gene therapy.
Although CRISPR-Cas technologies revolutionized genome editing in eukaryotes because of simplicity and programmability, they have not been as widely favored for bacterial genome editing.
The discovery and applications of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas based technologies have revolutionized genome editing in eukaryotic organisms due to its simplicity and programmability. Nevertheless, this system has not been as widely favored for bacterial genome editing.
Section: abstract
The review addresses fluorescent-protein-based methods for evaluating the efficacy of CRISPR-based genome-editing systems in bacteria.
Finally, we also address fluorescent-protein-based methods to evaluate the efficacy of CRISPR-based systems for genome editing in bacteria.
Section: abstract
The review addresses fluorescent-protein-based methods for evaluating the efficacy of CRISPR-based genome-editing systems in bacteria.
Finally, we also address fluorescent-protein-based methods to evaluate the efficacy of CRISPR-based systems for genome editing in bacteria.
Section: abstract
The review addresses fluorescent-protein-based methods for evaluating the efficacy of CRISPR-based genome-editing systems in bacteria.
Finally, we also address fluorescent-protein-based methods to evaluate the efficacy of CRISPR-based systems for genome editing in bacteria.
Section: abstract
The review addresses fluorescent-protein-based methods for evaluating the efficacy of CRISPR-based genome-editing systems in bacteria.
Finally, we also address fluorescent-protein-based methods to evaluate the efficacy of CRISPR-based systems for genome editing in bacteria.
Section: abstract
The review addresses fluorescent-protein-based methods for evaluating the efficacy of CRISPR-based genome-editing systems in bacteria.
Finally, we also address fluorescent-protein-based methods to evaluate the efficacy of CRISPR-based systems for genome editing in bacteria.
Section: abstract
The review addresses fluorescent-protein-based methods for evaluating the efficacy of CRISPR-based genome-editing systems in bacteria.
Finally, we also address fluorescent-protein-based methods to evaluate the efficacy of CRISPR-based systems for genome editing in bacteria.
Section: abstract
The review addresses fluorescent-protein-based methods for evaluating the efficacy of CRISPR-based genome-editing systems in bacteria.
Finally, we also address fluorescent-protein-based methods to evaluate the efficacy of CRISPR-based systems for genome editing in bacteria.
Section: abstract
Bacterial genome editing includes laborious and multi-step methods such as suicide plasmids.
Genome editing in bacteria encompasses a wide array of laborious and multi-step methods such as suicide plasmids.
Section: abstract
Bacterial genome editing includes laborious and multi-step methods such as suicide plasmids.
Genome editing in bacteria encompasses a wide array of laborious and multi-step methods such as suicide plasmids.
Section: abstract
Bacterial genome editing includes laborious and multi-step methods such as suicide plasmids.
Genome editing in bacteria encompasses a wide array of laborious and multi-step methods such as suicide plasmids.
Section: abstract
Bacterial genome editing includes laborious and multi-step methods such as suicide plasmids.
Genome editing in bacteria encompasses a wide array of laborious and multi-step methods such as suicide plasmids.
Section: abstract
Bacterial genome editing includes laborious and multi-step methods such as suicide plasmids.
Genome editing in bacteria encompasses a wide array of laborious and multi-step methods such as suicide plasmids.
Section: abstract
Bacterial genome editing includes laborious and multi-step methods such as suicide plasmids.
Genome editing in bacteria encompasses a wide array of laborious and multi-step methods such as suicide plasmids.
Section: abstract
Bacterial genome editing includes laborious and multi-step methods such as suicide plasmids.
Genome editing in bacteria encompasses a wide array of laborious and multi-step methods such as suicide plasmids.
Section: abstract
CRISPR-Cas still holds promise as a generalized genome-editing tool in bacteria and is undergoing further optimization for expanded application in these organisms.
CRISPR-Cas still holds promise as a generalized genome-editing tool in bacteria and is developing further optimization for an expanded application in these organisms.
Section: abstract
The review summarizes main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and presents alternatives intended to circumvent these issues.
In this review, we summarize the main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and present some alternatives to circumvent these issues, including CRISPR nickases, Cas12a, base editors, CRISPR-associated transposases, prime-editing, endogenous CRISPR systems, and the use of pre-made ribonucleoprotein complexes of Cas proteins and guide RNAs.
Section: abstract
The review summarizes main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and presents alternatives intended to circumvent these issues.
In this review, we summarize the main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and present some alternatives to circumvent these issues, including CRISPR nickases, Cas12a, base editors, CRISPR-associated transposases, prime-editing, endogenous CRISPR systems, and the use of pre-made ribonucleoprotein complexes of Cas proteins and guide RNAs.
Section: abstract
The review summarizes main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and presents alternatives intended to circumvent these issues.
In this review, we summarize the main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and present some alternatives to circumvent these issues, including CRISPR nickases, Cas12a, base editors, CRISPR-associated transposases, prime-editing, endogenous CRISPR systems, and the use of pre-made ribonucleoprotein complexes of Cas proteins and guide RNAs.
Section: abstract
The review summarizes main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and presents alternatives intended to circumvent these issues.
In this review, we summarize the main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and present some alternatives to circumvent these issues, including CRISPR nickases, Cas12a, base editors, CRISPR-associated transposases, prime-editing, endogenous CRISPR systems, and the use of pre-made ribonucleoprotein complexes of Cas proteins and guide RNAs.
Section: abstract
The review summarizes main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and presents alternatives intended to circumvent these issues.
In this review, we summarize the main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and present some alternatives to circumvent these issues, including CRISPR nickases, Cas12a, base editors, CRISPR-associated transposases, prime-editing, endogenous CRISPR systems, and the use of pre-made ribonucleoprotein complexes of Cas proteins and guide RNAs.
Section: abstract
The review summarizes main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and presents alternatives intended to circumvent these issues.
In this review, we summarize the main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and present some alternatives to circumvent these issues, including CRISPR nickases, Cas12a, base editors, CRISPR-associated transposases, prime-editing, endogenous CRISPR systems, and the use of pre-made ribonucleoprotein complexes of Cas proteins and guide RNAs.
Section: abstract
The review summarizes main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and presents alternatives intended to circumvent these issues.
In this review, we summarize the main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and present some alternatives to circumvent these issues, including CRISPR nickases, Cas12a, base editors, CRISPR-associated transposases, prime-editing, endogenous CRISPR systems, and the use of pre-made ribonucleoprotein complexes of Cas proteins and guide RNAs.
Section: abstract
Approval Evidence
15 sources36 linked approval claimsfirst-pass slugs phycoerythrin, prime-editing
next-generation, DSB-free base and prime editors reduce or eliminate the DSB-associated genotoxic stress observed with nuclease cutting
Source:
Regarding advances in b3-globin editing, "prime editing", although still in the experimental phase, has recently emerged as an innovative approach capable of introducing multiple HPFH-like mutations within b3-globin promoters, expanding future therapeutic possibilities in SCD.
Source:
The integration of new approaches, such as promoter engineering and Prime Editing, promises to further enhance the precision of genetic modifications, minimizing pleiotropic effects.
Source:
Prime editing is a versatile "search-and-replace" genome-editing technology that enables precise and flexible genome correction of genetic sequences by reverse-transcribing an RNA template encoded at the 3' end of a prime editing guide RNA (pegRNA).
Source:
Recent breakthroughs in precision genome editing, particularly base editing (BE) and prime editing (PE), have provided alternatives capable of directly correcting pathogenic variants. PE further allows for precise insertions and deletions.
Source:
Future directions in ocular gene therapy include the development of precision genome editing techniques, such as prime editing, miRNA-based regulation, and combinatorial approaches integrating gene therapy with stem cell transplantation or neuroprotective agents.
Source:
Advanced modalities, including base and prime editing, CRISPRi/a, and RNA-targeting Cas systems, improve precision and reduce genomic damage
Source:
Genome-editing innovations-such as prime, base, and epigenome editing-facilitate precise and reversible modulation of psychiatric risk genes.
Source:
Prime editing is an advanced genome editing technology that enables precise genetic modifications without inducing double-strand breaks or requiring donor DNA templates.
Source:
This review highlights the progression of organoid technologies, emphasizing the integration of genetic tools, including CRISPR-Cas9, prime editing, and lineage tracing.
Source:
Emerging gene editing technologies, such as CRISPR/Cas systems, base editing, and prime editing, offer novel approaches to optimize CAR-T cells
Source:
Emerging innovations, including base editing, prime editing, and novel nucleases like Cas12a and Cas13d, are expanding the functional genome-editing landscape.
Source:
application feasibilitysupports
Recent work in retinal cells and animal models has demonstrated growing feasibility of prime editing for inherited retinal disease treatment, modulation of pathological angiogenesis, and precise gene repair in post-mitotic photoreceptors and retinal pigment epithelial cells.
Source:
application scopesupports
Prime editing is particularly relevant to ophthalmology because many blinding disorders arise from point mutations or small indels that are well suited to prime-editing correction.
Source:
capability summarysupports
Prime editing enables precise genome correction by reverse-transcribing a template encoded in a pegRNA and can introduce substitutions and small indels in living cells without double-stranded DNA breaks or exogenous donor templates.
Source:
comparison scopesupports
The review compares prime editing with CRISPR-Cas9 and Base editing as gene-editing strategies for HbF modulation.
This review also provides a comparative overview of prime editing and other gene-editing strategies for HbF modulation, such as CRISPR-Cas9 and Base editing.
Source:
design objectivesupports
Next-generation precision engineering tools are proposed to enhance three efficacy pillars in CAR-NK cells: persistence, trafficking, and tumor eradication.
These advanced technologies enable the precise enhancement of three fundamental pillars of efficacy: Persistence through endogenous cytokine armoring and metabolic engineering; Trafficking via chemokine receptor matching and stromal barrier degradation; and Tumor Eradication using logic-gated targeting, immunomodulatory payloads, and bispecific engagers.
Source:
engineering capabilitysupports
Prime editing has emerged as an experimental approach capable of introducing multiple HPFH-like mutations within b3-globin promoters.
Regarding advances in b3-globin editing, "prime editing", although still in the experimental phase, has recently emerged as an innovative approach capable of introducing multiple HPFH-like mutations within b3-globin promoters...
Source:
future promisesupports
Promoter engineering and Prime Editing are expected to improve precision of soybean genetic modification and minimize pleiotropic effects.
The integration of new approaches, such as promoter engineering and Prime Editing, promises to further enhance the precision of genetic modifications, minimizing pleiotropic effects.
Source:
mechanistic advantagesupports
DSB-free base and prime editors reduce or eliminate DSB-associated genotoxic stress compared with nuclease cutting.
next-generation, DSB-free base and prime editors reduce or eliminate the DSB-associated genotoxic stress observed with nuclease cutting
Source:
optimization summarysupports
Engineering of Cas9 and reverse transcriptase domains, refinement of pegRNA architecture, recruitment of auxiliary proteins, and modulation of DNA repair pathways have enhanced prime-editing efficiency, product purity, and target scope across diverse cell types and tissues.
Source:
performance trendsupports
Prime editor generations from PE1 to PE7 and other next-generation variants are reported in the review to have increased in vitro editing efficiencies from 0.7 to 5.5% to more than 50%.
Source:
translational outlooksupports
As delivery vectors and newer prime editor variants improve, prime editing is presented as a plausible next-generation platform for a wide range of ocular diseases.
Source:
applicabilitysupports
Structural modifications and improved delivery methods have expanded prime editing applicability across eukaryotic systems.
Through structural modifications and improved delivery methods, prime editing has expanded its applicability across eukaryotic systems.
Source:
application claimsupports
CRISPR/Cas systems, base editing, and prime editing offer novel approaches to optimize CAR-T cells.
Source:
application scopesupports
Design biology advances including artificial cells, DNA nanostructures, AI-driven molecular design, biofoundries, and next-generation genome editing are transforming mind-body health sciences.
Source:
capabilitysupports
Base editing and prime editing provide alternatives for directly correcting pathogenic variants in inherited retinal diseases.
Recent breakthroughs in precision genome editing, particularly base editing (BE) and prime editing (PE), have provided alternatives capable of directly correcting pathogenic variants.
Source:
capabilitysupports
Prime editing, base editing, and epigenome editing facilitate precise and reversible modulation of psychiatric risk genes.
Source:
capabilitysupports
Prime editing enables precise genetic modifications without inducing double-strand breaks or requiring donor DNA templates.
Prime editing is an advanced genome editing technology that enables precise genetic modifications without inducing double-strand breaks or requiring donor DNA templates.
Source:
comparative advantagesupports
Base editing and prime editing circumvent double-strand DNA cleavage or repair processes typically induced by conventional CRISPR-Cas editing systems, offering advantages in post-mitotic retinal cells.
both circumventing the double-strand DNA cleavage or repair processes typically induced by conventional CRISPR-Cas editing systems, thereby offering advantages in post-mitotic retinal cells
Source:
contextual combinationsupports
The utility of next-generation genome editing for psychiatric risk gene modulation is particularly highlighted when combined with iPSC and brain-organoid models.
Source:
engineering advancesupports
Recent prime editing innovations enhance editing efficiency.
Here we examine the evolution of prime editing technologies, detailing advancements from the initial prime editing systems to recent innovations that enhance editing efficiency.
Source:
Comparisons
Source-stated alternatives
The abstract contrasts prime editing with editing approaches that require double-stranded DNA breaks or exogenous donor templates, but does not name specific alternative platforms.; The abstract mentions promoter engineering, RNAi, CRISPR/Cas9, AlphaFold2-guided gene editing, transgenesis, and induced mutagenesis.; The abstract explicitly contrasts prime editing with CRISPR-Cas9 and Base editing as other gene-editing strategies for HbF modulation.; The abstract contrasts prime editing with DSB-based CRISPR-Cas9 and also mentions base editing, targeted transposon systems, and synthetic or epigenetic circuits.; The abstract groups prime editing with base editing and novel nucleases such as Cas12a and Cas13d.; The abstract mentions CRISPR/Cas systems and base editing as alternative gene editing approaches.; CRISPR-Cas9 and lineage tracing are named as other genetic approaches emphasized by the review.; The abstract contrasts prime editing with approaches that induce double-strand breaks or require donor DNA templates, but it does not name specific alternative methods.; The same future-direction sentence mentions miRNA-based regulation and combinatorial approaches as other forward-looking strategies.; The abstract contrasts prime editing with gene augmentation strategies and conventional CRISPR-Cas editing systems. It also discusses base editing as a related precision editing platform.; Base editing and gene silencing are explicitly named as nearby strategies in the review.
Source:
The abstract contrasts prime editing with editing approaches that require double-stranded DNA breaks or exogenous donor templates, but does not name specific alternative platforms.
Source:
The abstract mentions promoter engineering, RNAi, CRISPR/Cas9, AlphaFold2-guided gene editing, transgenesis, and induced mutagenesis.
Source:
The abstract explicitly contrasts prime editing with CRISPR-Cas9 and Base editing as other gene-editing strategies for HbF modulation.
Source:
The abstract contrasts prime editing with DSB-based CRISPR-Cas9 and also mentions base editing, targeted transposon systems, and synthetic or epigenetic circuits.
Source:
The abstract groups prime editing with base editing and novel nucleases such as Cas12a and Cas13d.
Source:
The abstract mentions CRISPR/Cas systems and base editing as alternative gene editing approaches.
Source:
CRISPR-Cas9 and lineage tracing are named as other genetic approaches emphasized by the review.
Source:
The abstract contrasts prime editing with approaches that induce double-strand breaks or require donor DNA templates, but it does not name specific alternative methods.
Source:
The same future-direction sentence mentions miRNA-based regulation and combinatorial approaches as other forward-looking strategies.
Source:
The abstract contrasts prime editing with gene augmentation strategies and conventional CRISPR-Cas editing systems. It also discusses base editing as a related precision editing platform.
Source:
Base editing and gene silencing are explicitly named as nearby strategies in the review.
Source-backed strengths
The evidence does not report any prime-editing-specific strengths. The only contextual statement is that CRISPR-Cas technologies have been less widely favored for bacterial genome editing than in eukaryotes, which does not establish a strength of prime editing itself.
Source:
The discovery and applications of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas based technologies have revolutionized genome editing in eukaryotic organisms due to its simplicity and programmability. Nevertheless, this system has not been as widely favored for bacterial genome editing.
Compared with base editing
The abstract explicitly contrasts prime editing with CRISPR-Cas9 and Base editing as other gene-editing strategies for HbF modulation.; The abstract contrasts prime editing with DSB-based CRISPR-Cas9 and also mentions base editing, targeted transposon systems, and synthetic or epigenetic circuits.; The abstract groups prime editing with base editing and novel nucleases such as Cas12a and Cas13d.; The abstract mentions CRISPR/Cas systems and base editing as alternative gene editing approaches.; The abstract contrasts prime editing with gene augmentation strategies and conventional CRISPR-Cas editing systems. It also discusses base editing as a related precision editing platform.; Base editing and gene silencing are explicitly named as nearby strategies in the review.
Shared frame: source-stated alternative in extracted literature
Strengths here: supports substitutions and indels in living cells; does not require double-stranded DNA breaks; does not require exogenous donor templates.
Relative tradeoffs: delivery vectors and newer variants still need improvement for translation; still in the experimental phase; future impact is expected to depend on efficiency.
Source:
The abstract explicitly contrasts prime editing with CRISPR-Cas9 and Base editing as other gene-editing strategies for HbF modulation.
Source:
The abstract contrasts prime editing with DSB-based CRISPR-Cas9 and also mentions base editing, targeted transposon systems, and synthetic or epigenetic circuits.
Source:
The abstract groups prime editing with base editing and novel nucleases such as Cas12a and Cas13d.
Source:
The abstract mentions CRISPR/Cas systems and base editing as alternative gene editing approaches.
Source:
The abstract contrasts prime editing with gene augmentation strategies and conventional CRISPR-Cas editing systems. It also discusses base editing as a related precision editing platform.
Source:
Base editing and gene silencing are explicitly named as nearby strategies in the review.
Compared with CRISPR/Cas9
The abstract mentions promoter engineering, RNAi, CRISPR/Cas9, AlphaFold2-guided gene editing, transgenesis, and induced mutagenesis.; The abstract explicitly contrasts prime editing with CRISPR-Cas9 and Base editing as other gene-editing strategies for HbF modulation.; The abstract contrasts prime editing with DSB-based CRISPR-Cas9 and also mentions base editing, targeted transposon systems, and synthetic or epigenetic circuits.; The abstract mentions CRISPR/Cas systems and base editing as alternative gene editing approaches.; CRISPR-Cas9 and lineage tracing are named as other genetic approaches emphasized by the review.; The abstract contrasts prime editing with gene augmentation strategies and conventional CRISPR-Cas editing systems. It also discusses base editing as a related precision editing platform.
Shared frame: source-stated alternative in extracted literature
Strengths here: supports substitutions and indels in living cells; does not require double-stranded DNA breaks; does not require exogenous donor templates.
Relative tradeoffs: delivery vectors and newer variants still need improvement for translation; still in the experimental phase; future impact is expected to depend on efficiency.
Source:
The abstract mentions promoter engineering, RNAi, CRISPR/Cas9, AlphaFold2-guided gene editing, transgenesis, and induced mutagenesis.
Source:
The abstract explicitly contrasts prime editing with CRISPR-Cas9 and Base editing as other gene-editing strategies for HbF modulation.
Source:
The abstract contrasts prime editing with DSB-based CRISPR-Cas9 and also mentions base editing, targeted transposon systems, and synthetic or epigenetic circuits.
Source:
The abstract mentions CRISPR/Cas systems and base editing as alternative gene editing approaches.
Source:
CRISPR-Cas9 and lineage tracing are named as other genetic approaches emphasized by the review.
Source:
The abstract contrasts prime editing with gene augmentation strategies and conventional CRISPR-Cas editing systems. It also discusses base editing as a related precision editing platform.
Compared with CRISPR/Cas9 system
The abstract mentions promoter engineering, RNAi, CRISPR/Cas9, AlphaFold2-guided gene editing, transgenesis, and induced mutagenesis.; The abstract explicitly contrasts prime editing with CRISPR-Cas9 and Base editing as other gene-editing strategies for HbF modulation.; The abstract contrasts prime editing with DSB-based CRISPR-Cas9 and also mentions base editing, targeted transposon systems, and synthetic or epigenetic circuits.; The abstract mentions CRISPR/Cas systems and base editing as alternative gene editing approaches.; CRISPR-Cas9 and lineage tracing are named as other genetic approaches emphasized by the review.; The abstract contrasts prime editing with gene augmentation strategies and conventional CRISPR-Cas editing systems. It also discusses base editing as a related precision editing platform.
Shared frame: source-stated alternative in extracted literature
Strengths here: supports substitutions and indels in living cells; does not require double-stranded DNA breaks; does not require exogenous donor templates.
Relative tradeoffs: delivery vectors and newer variants still need improvement for translation; still in the experimental phase; future impact is expected to depend on efficiency.
Source:
The abstract mentions promoter engineering, RNAi, CRISPR/Cas9, AlphaFold2-guided gene editing, transgenesis, and induced mutagenesis.
Source:
The abstract explicitly contrasts prime editing with CRISPR-Cas9 and Base editing as other gene-editing strategies for HbF modulation.
Source:
The abstract contrasts prime editing with DSB-based CRISPR-Cas9 and also mentions base editing, targeted transposon systems, and synthetic or epigenetic circuits.
Source:
The abstract mentions CRISPR/Cas systems and base editing as alternative gene editing approaches.
Source:
CRISPR-Cas9 and lineage tracing are named as other genetic approaches emphasized by the review.
Source:
The abstract contrasts prime editing with gene augmentation strategies and conventional CRISPR-Cas editing systems. It also discusses base editing as a related precision editing platform.
Compared with microRNA
The same future-direction sentence mentions miRNA-based regulation and combinatorial approaches as other forward-looking strategies.
Shared frame: source-stated alternative in extracted literature
Strengths here: supports substitutions and indels in living cells; does not require double-stranded DNA breaks; does not require exogenous donor templates.
Relative tradeoffs: delivery vectors and newer variants still need improvement for translation; still in the experimental phase; future impact is expected to depend on efficiency.
Source:
The same future-direction sentence mentions miRNA-based regulation and combinatorial approaches as other forward-looking strategies.
Compared with miRNA-based regulation
The same future-direction sentence mentions miRNA-based regulation and combinatorial approaches as other forward-looking strategies.
Shared frame: source-stated alternative in extracted literature
Strengths here: supports substitutions and indels in living cells; does not require double-stranded DNA breaks; does not require exogenous donor templates.
Relative tradeoffs: delivery vectors and newer variants still need improvement for translation; still in the experimental phase; future impact is expected to depend on efficiency.
Source:
The same future-direction sentence mentions miRNA-based regulation and combinatorial approaches as other forward-looking strategies.
Ranked Citations
- 1.
- 2.
- 3.
- 4.
- 5.
- 6.
- 7.
- 8.
- 9.
- 10.
- 11.
- 12.